-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Tom, Thank you very much for checking this and for the explanation. If I understand correctly a full omit map like the one I wanted (with no rebuilding) might be useful to check, possibly at the end of refinement, whether there is significant bias. This should give similar information than the sfcheck omit map. However, we wanted to check a particular region of the model where the density is poor and not really improving with refinement. Hence, we wanted to ponder if there was bias but with the aim of building a new model for that region if required. Am I correct at deducing from your explanation that for this case it would be preferable calculating the full omit *with* iterative model-building? Cheers, Miguel En/na Thomas C. Terwilliger ha escrit:
Hi Jianghai,
The phenix full_omit map, if calculated with no model-building, is similar to both the SFCHECK map and the CNS composite SA-OMIT map.
The phenix full_omit map removes atoms in each omit box and in a 2 A radius around the omit box, then calculates phases, then puts all the omitted regions together. This is like the CNS SA-omit map with no simulated annealing. It is also like the SFCHECK OMIT map, except that SFCHECK does not remove atoms 2 A around the box.
The real power of the full_omit map is to calculate it WITH iterative model-building. In this case the atoms that get built inside the omit region get an occupancy of 0.0 each cycle. The model outside the omit region gets better and better, so that the omit density gets improved every cycle. Then when all the omit regions are recombined, the map is totally unbiased, but it can be much better than the starting omit map.
-Tom T
Is this map a total OMIT map like SFCHECK does or a SA-OMIT map like CNS does?
Jianghai
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